From d868e56b6876e19b5236c6409a12a811fa5b51b3 Mon Sep 17 00:00:00 2001
From: DSilva27 <david.silvas@udea.edu.co>
Date: Thu, 16 Mar 2023 10:34:18 -0700
Subject: [PATCH] update README

---
 README.md  | 45 -------------------------------------
 README.rst | 66 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 66 insertions(+), 45 deletions(-)
 delete mode 100644 README.md
 create mode 100644 README.rst

diff --git a/README.md b/README.md
deleted file mode 100644
index 903aa69..0000000
--- a/README.md
+++ /dev/null
@@ -1,45 +0,0 @@
-[![](https://github.com/DSilva27/cryo_em_SBI/blob/iss6/.github/workflows/python-package.yml/badge.svg)](https://github.com/DSilva27/cryo_em_SBI/actions)
-# cryo_em_SBI
-
-
-## Collaborators
-
-
-David Silva-Sánchez, Lars Dingeldein, Roberto Covino, Pilar Cossio
-
-# Dependencies
-
-1. Lampe
-2. SciPy
-3. NumPy
-4. PyTorch
-5. json
-
-# Installing
-
-## Download this repository
-
-`https://github.com/DSilva27/cryo_em_SBI.git`
-
-## Install the module
-`python3 -m pip install -e .`
-
-# Using the code
-
-
-## Generating data from command line
-
-```bash
-python3 -m cryo_sbi.generate_training_set --config_file experiments/benchmark_hsp90/image_params_snr01_128.json --num_train_samples 10 --num_val_samples 10 --file_name "test1" --n_workers 24
-```
-
-## Train posterior from command line
-
-```bash
-python3 -m cryo_sbi.inference.NPE_train_without_saving \
-    --image_config_file experiments/benchmark_hsp90/image_params_training.json \
-    --train_config_file experiments/benchmark_hsp90/resnet18_encoder.json\
-    --epochs 100 \
-    --estimator_file experiments/benchmark_hsp90/posterior_hsp90.estimator \
-    --loss_file experiments/benchmark_hsp90/posterior_hsp90.loss 
-```
\ No newline at end of file
diff --git a/README.rst b/README.rst
new file mode 100644
index 0000000..1bb4713
--- /dev/null
+++ b/README.rst
@@ -0,0 +1,66 @@
+===========
+cryo_em_SBI
+===========
+
+.. start-badges
+
+.. list-table::
+    :stub-columns: 1
+
+    * - tests
+      - | |githubactions|
+        
+
+.. |githubactions| image:: https://github.com/DSilva27/cryo_em_SBI/actions/workflows/python-package.yml/badge.svg?branch=iss6
+    :alt: Testing Status
+    :target: https://github.com/DSilva27/cryo_em_SBI/actions
+
+Collaborators
+-------------
+
+David Silva-Sánchez, Lars Dingeldein, Roberto Covino, Pilar Cossio
+
+Dependencies
+------------
+
+1. Lampe
+2. SciPy
+3. NumPy
+4. PyTorch
+5. json
+
+Installing
+----------
+
+Download this repository
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+`https://github.com/DSilva27/cryo_em_SBI.git`
+
+Install the module
+~~~~~~~~~~~~~~~~~~
+::
+    python3 -m pip install .
+
+Using the code
+==============
+
+Generating data from command line
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. code:: bash
+
+    python3 -m cryo_sbi.generate_training_set --config_file experiments/benchmark_hsp90/image_params_snr01_128.json --num_train_samples 10 --num_val_samples 10 --file_name "test1" --n_workers 24
+
+
+Train posterior from command line
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. code:: bash
+
+    python3 -m cryo_sbi.inference.NPE_train_without_saving \
+        --image_config_file experiments/benchmark_hsp90/image_params_training.json \
+        --train_config_file experiments/benchmark_hsp90/resnet18_encoder.json\
+        --epochs 100 \
+        --estimator_file experiments/benchmark_hsp90/posterior_hsp90.estimator \
+        --loss_file experiments/benchmark_hsp90/posterior_hsp90.loss